Li, Zhiguang, Su, Zhenqiang, Wen, Zhining, Shi, Leming, Chen, Tao
Abstract Background Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and...
Bmc Bioinformatics, Zhenqiang Su, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins, ...
Proceedings Very Important Pool (VIP) genes – an application for microarray-based molecular signatures
Bmc Bioinformatics, Hapmap Samples, Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, ...
Proceedings Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270
Fan, Xiaohui, Shi, Leming, Fang, Hong, Harris, Stephen, Perkins, Roger, Tong, Weida
Abstract Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar...
Weida Tong, Qian Xie, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins, ...
Class prediction using “omics ” data is playing an increasing role in toxicogenomics, diagnosis/prognosis, and risk assessment. These data are usually noisy and represented by relatively few...
Very Important Pool (VIP) genes – an application for microarray-based molecular signatures (2008)
Su, Zhenqiang, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, Tong, Weida
Abstract Background Advances in DNA microarray technology portend that molecular signatures from which microarray will eventually be used in clinical environments and personalized medicine....
Hong, Huixiao, Su, Zhenqiang, Ge, Weigong, Shi, Leming, Perkins, Roger, Fang, Hong, ...
Abstract Background Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with...
Shi, Leming, Jones, Wendell D, Jensen, Roderick V, Harris, Stephen C, Perkins, Roger G, Goodsaid, Federico M, ...
Abstract Background Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially...
cytotoxicity for identification of biomarkers (2008)
Yongxi Tan, Leming Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M, ...
Integrating time-course microarray gene expression profiles with
Bmc Bioinformatics, Tao Han, Cathy D Melvin, Leming Shi, William S Branham, Carrie L Mol, ...
© 2006 Han et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies (2007)
Leming Shi, Wendell D. Jones, Roderick V. Jensen, Stephen C. Harris, Roger G. Perkins, Federico M. Goodsaid, ...
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent...
Variability of DNA Microarray Gene Expression Profiles in Cultured Rat Primary Hepatocytes (2007)
Jun Xu, Xutao Deng, Victor Chan, Nancy Kelley-Loughnane, Brent W Harker, Leming Shi, ...
DNA microarray is a powerful tool in biomedical research. However, transcriptomic profiling using DNA microarray is subject to many variations including biological variability. To evaluate the...
Mei, Nan, Guo, Lei, Zhang, Lu, Shi, Leming, Sun, Yongming, Fung, Chris, ...
Abstract Background Comfrey is consumed by humans as a vegetable and a tea, and has been used as an herbal medicine for more than 2000 years. Comfrey, however, is hepatotoxic in livestock and humans...
Han, Tao, Melvin, Cathy D, Shi, Leming, Branham, William S, Moland, Carrie L, Pine, P Scott, ...
Abstract Background DNA microarrays, which have been increasingly used to monitor mRNA transcripts at a global level, can provide detailed insight into cellular processes involved in response to...
Guo, Lei, Fang, Hong, Collins, Jim, Fan, Xiao-hui, Dial, Stacey, Wong, Alex, ...
Abstract Background Fibrates are a unique hypolipidemic drugs that lower plasma triglyceride and cholesterol levels through their action as peroxisome proliferator-activated receptor alpha (PPARα)...
Chen, Tao, Guo, Lei, Zhang, Lu, Shi, Leming, Fang, Hong, Sun, Yongming, ...
Abstract Background Aristolochic acid (AA) is the active component of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. AA, however, induced...
Tan, Yongxi, Shi, Leming, Hussain, Saber M., Xu, Jun, Tong, Weida, Frazier, John M., ...
Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity...
Bmc Bioinformatics, Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey Dial, ...
Proceedings Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor α agonists
Microarray scanner calibration curves: characteristics and implications (2005)
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Abstract Background Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration...
Shi, Leming, Tong, Weida, Fang, Hong, Scherf, Uwe, Han, Jing, Puri, Raj K, ...
Abstract Background The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E....
Hong, Huixiao, Dragan, Yvonne, Epstein, Joshua, Teitel, Candee, Chen, Bangzheng, Xie, Qian, ...
Abstract Background Proteomic profiling of complex biological mixtures by the ProteinChip technology of surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS)...
Xu, Zengjun, Patterson, Tucker A, Wren, Jonathan D, Han, Tao, Shi, Leming, Duhart, Helen, ...
Abstract Background This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium...
Tan, Yongxi, Shi, Leming, Tong, Weida, Wang, Charles
DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One...
Tan, Yongxi, Shi, Leming, Hussain, Saber M., Xu, Jun, Tong, Weida, Frazier, John M., ...
Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity...
A microarray study of MPP +-treated PC12 Cells: Mechanisms of (2005)
Bmc Bioinformatics, Zengjun Xu, Tucker A Patterson, Jonathan D Wren, Tao Han, Leming Shi, ...
Proceedings
Weida Tong, Xiaoxi Cao, Stephen Harris, Hongmei Sun, Hong Fang, James Fuscoe, ...
The mapping of the human genome and the determination of corresponding gene functions, pathways, and biological mechanisms are driving the emergence of the new research fields of toxicogenomics and...
Blair, Robert M., Fang, Hong, Branham, William S., Hass, Bruce S., Dial, Stacey L., Moland, Carrie L., ...
We have utilized a validated (standardized) estrogen receptor (ER) competitive-binding assay to determine the ER affinity for a large, structurally diverse group of chemicals. Uteri from...
Tan, Yongxi, Shi, Leming, Tong, Weida, Wang, Charles
DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One...
Hong, Huixiao, Tong, Weida, Fang, Hong, Shi, Leming, Xie, Qian, Wu, Jie, ...
A number of environmental chemicals, by mimicking natural hormones, can disrupt endocrine function in experimental animals, wildlife, and humans. These chemicals, called "endocrine-disrupting...
Tong, Weida, Cao, Xiaoxi, Harris, Stephen, Sun, Hongmei, Fang, Hong, Fuscoe, James, ...
The mapping of the human genome and the determination of corresponding gene functions, pathways, and biological mechanisms are driving the emergence of the new research fields of toxicogenomics and...
Tong, Weida, Xie, Qian, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, ...
Class prediction using “omics” data is playing an increasing role in toxicogenomics, diagnosis/prognosis, and risk assessment. These data are usually noisy and represented by relatively few...
Tong, Weida, Xie, Qian, Hong, Huixiao, Shi, Leming, Fang, Hong, Perkins, Roger
Quantitative structure–activity relationship (QSAR) methods have been widely applied in drug discovery, lead optimization, toxicity prediction, and regulatory decisions. Despite major advances in...
Microarray scanner calibration curves: characteristics and implications
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Chen, Tao, Guo, Lei, Zhang, Lu, Shi, Leming, Fang, Hong, Sun, Yongming, ...
Tan, Yongxi, Shi, Leming, Tong, Weida, Wang, Charles
DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One...
Hong, Huixiao, Tong, Weida, Fang, Hong, Shi, Leming, Xie, Qian, Wu, Jie, ...
A number of environmental chemicals, by mimicking natural hormones, can disrupt endocrine function in experimental animals, wildlife, and humans. These chemicals, called "endocrine-disrupting...
Tong, Weida, Cao, Xiaoxi, Harris, Stephen, Sun, Hongmei, Fang, Hong, Fuscoe, James, ...
The mapping of the human genome and the determination of corresponding gene functions, pathways, and biological mechanisms are driving the emergence of the new research fields of toxicogenomics and...
Tong, Weida, Xie, Qian, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, ...
Class prediction using “omics” data is playing an increasing role in toxicogenomics, diagnosis/prognosis, and risk assessment. These data are usually noisy and represented by relatively few...
Tong, Weida, Xie, Qian, Hong, Huixiao, Shi, Leming, Fang, Hong, Perkins, Roger
Quantitative structure–activity relationship (QSAR) methods have been widely applied in drug discovery, lead optimization, toxicity prediction, and regulatory decisions. Despite major advances in...
Microarray scanner calibration curves: characteristics and implications
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Chen, Tao, Guo, Lei, Zhang, Lu, Shi, Leming, Fang, Hong, Sun, Yongming, ...
Very Important Pool (VIP) genes – an application for microarray-based molecular signatures
Su, Zhenqiang, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, Tong, Weida
Shi, Leming, Jones, Wendell D, Jensen, Roderick V, Harris, Stephen C, Perkins, Roger G, Goodsaid, Federico M, ...
Fan, Xiaohui, Shi, Leming, Fang, Hong, Harris, Stephen, Perkins, Roger, Tong, Weida
Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar studies...